Related papers: Representing catalytic mechanisms with rule compos…

The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional…

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning…

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state…

Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

Graph-Rewriting Automata (GRA) are an extension of Cellular Automata to a dynamic structure using local graph-rewriting rules. This work introduces linear algebra based tools that allow for a practical investigation of their behavior in…

Graph-based modeling plays a fundamental role in many areas of computer science. In this paper, we introduce systems of graph formulas with variables for specifying graph properties; this notion generalizes the graph formulas introduced in…

Reactive synthesis is an automatic way to translate a human intention expressed in some logic into a system of some kind. This thesis has two parts, devoted to logic and to systems. In Part I, we develop two new approaches to CTL*…

Time-continuous dynamical systems defined on graphs are often used to model complex systems with many interacting components in a non-spatial context. In the reverse sense attaching meaningful dynamics to given 'interaction diagrams' is a…

Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…

We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…

Understanding the set of elementary steps and kinetics in each reaction is extremely valuable to make informed decisions about creating the next generation of catalytic materials. With physical and mechanistic complexity of industrial…

I introduce a formalism for representing the syntax of recursively structured graph-like patterns. It does not use production rules, like a conventional graph grammar, but represents the syntactic structure in a more direct and declarative…

In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…

Here we focus on the challenge of verifying the correctness of molecular implementations of abstract chemical reaction networks, where operation in a well-mixed "soup" of molecules is stochastic, asynchronous, concurrent, and often involves…

Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG…

Automatic Robotic Assembly Sequence Planning (RASP) can significantly improve productivity and resilience in modern manufacturing along with the growing need for greater product customization. One of the main challenges in realizing such…

Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…

Many graph algorithms can be viewed as sets of rules that are iteratively applied, with the number of iterations dependent on the size and complexity of the input graph. Existing machine learning architectures often struggle to represent…